Align Citrate-proton symporter; Citrate carrier protein; Citrate transporter; Citrate utilization determinant; Citrate utilization protein A (characterized)
to candidate AO353_15110 AO353_15110 MFS transporter
Query= SwissProt::P0A2G3 (434 letters) >FitnessBrowser__pseudo3_N2E3:AO353_15110 Length = 448 Score = 293 bits (749), Expect = 1e-83 Identities = 154/414 (37%), Positives = 237/414 (57%), Gaps = 12/414 (2%) Query: 5 TPATSRAGTFGAILRVTSGNFLEQFDFFLFGFYATYIARTFFPAESEFASLMLTFAVFGS 64 TP + F +L GN +E FDF ++ +A I TFFP++S F SLML+ FG+ Sbjct: 17 TPGAGKKSIFAVVL----GNAVEFFDFGVYATFAVMIGHTFFPSDSAFVSLMLSVIAFGT 72 Query: 65 GFLMRPVGAIVLGAYIDRIGRRKGLMVTLAIMGCGTLLIALVPGYQTIGLAAPALVLLGR 124 GF++RP+GA+++GAY DR+GR+ +++TL +M GT IA++PGY+TIG+AAP L+++ R Sbjct: 73 GFIVRPLGAVLIGAYADRVGRKPAMLLTLVMMAVGTGSIAILPGYETIGIAAPILLVVTR 132 Query: 125 LLQGFSAGVELGGVSVYLSEIATPGNKGFYTSWQSASQQVAIVVAALIGYSLNITLGHDA 184 ++QG + G E G + Y+ E A P +G Y WQ +Q VA +VA L+G++L L + Sbjct: 133 MIQGLAWGGEAGPATTYILEAAPPHKRGTYACWQVVAQGVAAMVAGLVGFTLTKVLSPED 192 Query: 185 ISEWGWRIPFFIGCMIIPLIFVLRRSLQETEAFLQRKHRPDTRE---IFATIAKNWRIIT 241 ++ WGWR+PF G +++P+ +RR+L ET H TR + + K+ R + Sbjct: 193 LNSWGWRVPFVFGLLVLPIGIYIRRNLAET----FHGHTEQTRTGDLVREIVGKHRRALV 248 Query: 242 AGTLLVAMTTTTFYFITVYTPTYGRTVLNLSARDSLIVTMLVGVSNFIWLPIGGAISDRI 301 G L+++ +T T YF+ Y T+ T L L +++ T++ G + + GG + DR Sbjct: 249 LGLLILSGSTITQYFLN-YMTTFALTELKLPTSIAMLSTLVAGAAMAVCAVAGGMLCDRF 307 Query: 302 GRRAVLMGITLLALITTWPVMQWLTAAPDFTRMTLVLLWFSFFFGMYNGAMVAALTEVMP 361 GRR +LM ++ L+ +P +Q +T P L L S GM A++ L E P Sbjct: 308 GRRVILMTPRVVLLLILFPALQLMTEHPSSATFLLTLAVLSGLHGMSGAALIVLLVESFP 367 Query: 362 VYVRTVGFSLAFSLATAIFGGLTPAISTALVKLTGDKSSPGWWLMCAALCGLAA 415 VR GFS+ ++ A FGG I T L+ TGD SP W+L+ A L L A Sbjct: 368 KSVRATGFSIVYAFGVAAFGGTAQIIITWLIGTTGDPMSPVWYLLIANLVCLTA 421 Lambda K H 0.329 0.140 0.432 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 529 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 434 Length of database: 448 Length adjustment: 32 Effective length of query: 402 Effective length of database: 416 Effective search space: 167232 Effective search space used: 167232 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory